Gene Regulation and Expression

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2015

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment

Gierlinski, M., Cole, C., Schofield, P., Schurch, N. J., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G., Owen-Hughes, T., Blaxter, M. & Barton, G. J., 15 Nov 2015, In : Bioinformatics. 31, 22, p. 3625-3630 6 p.

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30 Citations (Scopus)
141 Downloads (Pure)

Structural basis for the RING catalyzed synthesis of K63 linked ubiquitin chains

Branigan, E., Plechanovova, A., Jaffray, E. G., Naismith, J. H. & Hay, R. T., Aug 2015, In : Nature Structural & Molecular Biology. 22, 8, p. 597-602 6 p.

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47 Citations (Scopus)
125 Downloads (Pure)

Targeted knock-down of miR21 primary transcripts using snoMEN vectors induces apoptosis in human cancer cell lines

Ono, M., Ono, K., Avolio, F., Afzal, V., Bensaddek, D. & Lamond, A. I., 25 Sep 2015, In : PLoS ONE. 10, 9, 22 p., e0138668.

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7 Citations (Scopus)
367 Downloads (Pure)

Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast

Køhler, J. B., Tammsalu, T., Jørgensen, M. M., Steen, N., Hay, R. T. & Thon, G., 2015, In : Nature Communications. 6, p. 1-14 14 p., 8827.

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14 Citations (Scopus)
97 Downloads (Pure)

The nucleoporin ALADIN regulates Aurora A localization to ensure robust mitotic spindle formation

Carvalhal, S., Abreu Ribeiro, S., Arocena, M., Kasciukovic, T., Temme, A., Koehler, K., Huebner, A. & Griffis, E. R., 1 Oct 2015, In : Molecular Biology of the Cell. 26, 19, p. 3424-3438 15 p.

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11 Citations (Scopus)
175 Downloads (Pure)

The role of hypoxia in inflammatory disease (Review)

Biddlestone, J., Bandarra, D. & Rocha, S., 1 Apr 2015, In : International Journal of Molecular Medicine. 35, 4, p. 859-869 11 p.

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65 Citations (Scopus)

Two distinct modes for propagation of histone PTMs across the cell cycle

Alabert, C., Barth, T. K., Reverón-Gómez, N., Sidoli, S., Schmidt, A., Jensen, O., Imhof, A. & Groth, A., 15 Mar 2015, In : Genes and Development. 29, 6, p. 585-590 6 p.

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135 Citations (Scopus)
80 Downloads (Pure)

Ubiquitin-C-terminal hydrolases cleave isopeptide and peptide-linked ubiquitin from structured proteins but do not edit ubiquitin homopolymers

Bett, J. S., Ritorto, M. S., Ewan, R., Jaffray, E. G., Virdee, S., Chin, J. W., Knebel, A., Kurz, T., Trost, M., Tatham, M. H. & Hay, R. T., 15 Mar 2015, In : Biochemical Journal. 466, 3, p. 489-498 10 p.

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16 Citations (Scopus)

Visualization of the Serratia type VI secretion system reveals unprovoked attacks and dynamic assembly

Gerc, A. J., Diepold, A., Trunk, K., Porter, M., Rickman, C., Armitage, J. P., Stanley-Wall, N. R. & Coulthurst, S. J., 29 Sep 2015, In : Cell Reports. 12, 12, p. 2131-2142 12 p.

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36 Citations (Scopus)
217 Downloads (Pure)
2014

Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription

Di Cerbo, V., Mohn, F., Ryan, D. P., Montellier, E., Kacem, S., Tropberger, P., Kallis, E., Holzner, M., Hoerner, L., Feldmann, A., Richter, F. M., Bannister, A. J., Mittler, G., Michaelis, J., Khochbin, S., Feil, R., Schuebeler, D., Owen-Hughes, T., Daujat, S. & Schneider, R., 25 Mar 2014, In : eLife. 3, e01632.

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57 Citations (Scopus)
332 Downloads (Pure)

A conserved and essential basic region mediates tRNA binding to the Elp1 subunit of the Saccharomyces cerevisiae Elongator complex

Di Santo, R., Bandau, S. & Stark, M. J. R., Jun 2014, In : Molecular Microbiology. 92, 6, p. 1227-1242 16 p.

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15 Citations (Scopus)
148 Downloads (Pure)

A dynamic microtubule cytoskeleton directs medial actomyosin function during tube formation

Booth, A. J. R., Blanchard, G. B., Adams, R. J. & Röper, K., 9 Jun 2014, In : Developmental Cell. 29, 5, p. 562-576 15 p.

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36 Citations (Scopus)
144 Downloads (Pure)

Analysis of Global RNA Synthesis at the Single Cell Level following Hypoxia

Biddlestone, J., Druker, J., Shmakova, A., Ferguson, G., Swedlow, J. R. & Rocha, S., 13 May 2014, In : JoVE: Journal of Visualized Experiments. 87, 7 p., e51420.

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2 Citations (Scopus)
135 Downloads (Pure)

ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome

Tinti, M., Madeira, F., Murugesan, G., Hoxhaj, G., Toth, R. & Mackintosh, C., 2014, In : Database: the Journal of Biological Databases and Curation. 2014, 15 p., bat085.

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24 Citations (Scopus)
162 Downloads (Pure)

A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells

Ly, T., Ahmad, Y., Shlien, A., Soroka, D., Mills, A., Emanuele, M. J., Stratton, M. R. & Lamond, A. I., 4 Mar 2014, In : eLife. 2014, 3, e01630.

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67 Citations (Scopus)
87 Downloads (Pure)

A role for the Cajal-body-associated SUMO isopeptidase USPL1 in snRNA transcription mediated by RNA polymerase II

Hutten, S., Chachami, G., Winter, U., Melchior, F. & Lamond, A. I., 1 Mar 2014, In : Journal of Cell Science. 127, 5, p. 1065-1078 14 p.

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26 Citations (Scopus)
187 Downloads (Pure)
Open Access
37 Citations (Scopus)

Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks

Albergante, L., Blow, J. J. & Newman, T. J., 2 Sep 2014, In : eLife. 3, p. 1-28 28 p., e02863.

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13 Citations (Scopus)
149 Downloads (Pure)

C. elegans whole genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency.

Meier, B., Cooke, S. L., Weiss, J., Bailly, A. P., Alexandrov, L. B., Marshall, J., Raine, K., Maddison, M., Anderson, E., Stratton, M. R., Gartner, A. & Campbell, P. J., 2014, In : Genome Research. 24, p. 1624-1636 14 p.

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78 Citations (Scopus)

Cell cycle progression in response to oxygen levels

Ortmann, B., Druker, J. & Rocha, S., Sep 2014, In : Cellular and Molecular Life Sciences. 71, 18, p. 3569-3582 14 p.

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29 Citations (Scopus)

Cezanne (OTUD7B) regulates HIF-1α homeostasis in a proteasome-independent manner

Bremm, A., Moniz, S., Mader, J., Rocha, S. & Komander, D., 1 Dec 2014, In : EMBO Reports. 15, 12, p. 1268-1277 10 p.

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41 Citations (Scopus)
56 Downloads (Pure)

Chromatin and oxygen sensing in the context of JmjC histone demethylases

Shmakova, A., Batie, M., Druker, J. & Rocha, S., 15 Sep 2014, In : Biochemical Journal. 462, 3, p. 385-395 11 p.

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42 Citations (Scopus)
143 Downloads (Pure)

Dss1 is a 26S proteasome ubiquitin receptor

Paraskevopoulos, K., Kriegenburg, F., Tatham, M. H., Rösner, H. I., Medina, B., Larsen, I. B., Brandstrup, R., Hardwick, K. G., Hay, R. T., Kragelund, B. B., Hartmann-Petersen, R. & Gordon, C., 6 Nov 2014, In : Molecular Cell. 56, 3, p. 453-461 9 p.

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43 Citations (Scopus)
120 Downloads (Pure)
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25 Citations (Scopus)

E3 ubiquitin ligase HOIP attenuates apoptotic cell death induced by cisplatin

MacKay, C., Carroll, E., Ibrahim, A. F. M., Garg, A., Inman, G. J., Hay, R. T. & Alpi, A. F., 15 Apr 2014, In : Cancer Research. 74, 8, p. 2246-2257 12 p.

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31 Citations (Scopus)

Erythropoietin guides multipotent hematopoietic progenitor cells toward an erythroid fate

Grover, A., Mancini, E., Moore, S., Mead, A. J., Atkinson, D., Rasmussen, K. D., O'Carroll, D., Jacobsen, S. E. W. & Nerlov, C., 10 Feb 2014, In : Journal of Experimental Medicine. 211, 2, p. 181-188 8 p.

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63 Citations (Scopus)
84 Downloads (Pure)

Family-wide analysis of poly(ADP-ribose) polymerase activity

Vyas, S., Matic, I., Uchima, L., Rood, J., Zaja, R., Hay, R. T., Ahel, I. & Chang, P., 21 Jul 2014, In : Nature Communications. 5, 13 p., 4426.

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167 Citations (Scopus)

FMDV replicons encoding green fluorescent protein are replication competent

Tulloch, F., Pathania, U., Luke, G. A., Nicholson, J., Stonehouse, N. J., Rowlands, D. J., Jackson, T., Tuthill, T., Haas, J., Lamond, A. I. & Ryan, M. D., 1 Dec 2014, In : Journal of Virological Methods. 209, p. 35-40 6 p.

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11 Citations (Scopus)
104 Downloads (Pure)
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11 Citations (Scopus)
162 Downloads (Pure)

Grow₂: The HIF system, energy homeostasis and the cell cycle

Moniz, S., Biddlestone, J. & Rocha, S., May 2014, In : Histology and Histopathology. 29, 5, p. 589-600 12 p.

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13 Citations (Scopus)

Having a direct look: analysis of DNA damage and repair mechanisms by next generation sequencing

Meier, B. & Gartner, A., 15 Nov 2014, In : Experimental Cell Research. 329, 1, p. 35-41 7 p.

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4 Citations (Scopus)
139 Downloads (Pure)

Hypoxia activates IKK-NF-κB and the immune response in Drosophila melanogaster

Bandarra, D., Biddlestone, J., Mudie, S., Muller, H. A. & Rocha, S., 2014, In : Bioscience Reports. 34, 4, p. 429-440 12 p., e00127.

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14 Citations (Scopus)
144 Downloads (Pure)

Identification of small molecule inhibitors of pre-mRNA splicing

Pawellek, A., McElroy, S., Samatov, T., Mitchell, L., Woodland, A., Ryder, U., Gray, D., Lührmann, R. & Lamond, A. I., 12 Dec 2014, In : Journal of Biological Chemistry. 289, 50, p. 34683-34698 16 p.

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37 Citations (Scopus)
233 Downloads (Pure)

Length-dependent anisotropic scaling of spindle shape

Young, S., Besson, S. & Welburn, J. P. I., 15 Dec 2014, In : Open Biology. 3, 12, p. 1217-1223 7 p.

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13 Citations (Scopus)
97 Downloads (Pure)
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3 Citations (Scopus)
161 Downloads (Pure)

Molecular brakes regulating mTORC1 activation in skeletal muscle following synergist ablation

Hamilton, D. L., Philp, A., MacKenzie, M. G., Patton, A., Towler, M. C., Gallagher, I. J., Bodine, S. C. & Baar, K., 15 Aug 2014, In : American Journal of Physiology, Endocrinology and Metabolism. 307, 4, p. E365-E373 9 p.

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20 Citations (Scopus)
120 Downloads (Pure)

Monitoring Keap1-Nrf2 interactions in single live cells

Baird, L., Swift, S., Llères, D. & Dinkova-Kostova, A. T., 1 Nov 2014, In : Biotechnology Advances. 32, 6, p. 1133-1144 12 p.

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67 Citations (Scopus)
311 Downloads (Pure)

Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components

Alabert, C., Bukowski-Wills, J. C., Lee, S. B., Kustatscher, G., Nakamura, K., De Lima Alves, F., Menard, P., Mejlvang, J., Rappsilber, J. & Groth, A., 23 Feb 2014, In : Nature Cell Biology. 16, 3, p. 281-291 11 p.

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155 Citations (Scopus)

NDK-1, the homolog of NM23-H1/H2 regulates cell migration and apoptotic engulfment in C. elegans

Fancsalszky, L., Monostori, E., Farkas, Z., Pourkarimi, E., Masoudi, N., Hargitai, B., Bosnar, M. H., Deželjin, M., Zsákai, A., Vellai, T., Mehta, A. & Takács-Vellai, K., 21 Mar 2014, In : PLoS ONE. 9, 3, 12 p., e92687.

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19 Citations (Scopus)
84 Downloads (Pure)

Near real-time processing of proteomics data using Hadoop.

Hillman, C., Ahmad, Y., Whitehorn, M. & Cobley, A., 14 Mar 2014, In : Big Data. 2, 1, p. 44-49 5 p.

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5 Citations (Scopus)
236 Downloads (Pure)

New histone supply regulates replication fork speed and PCNA unloading

Mejlvang, J., Feng, Y., Alabert, C., Neelsen, K. J., Jasencakova, Z., Zhao, X., Lees, M., Sandelin, A., Pasero, P., Lopes, M. & Groth, A., 6 Jan 2014, In : Journal of Cell Biology. 204, 1, p. 29-43 15 p.

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71 Citations (Scopus)
90 Downloads (Pure)

Oligoasthenoteratozoospermia and Infertility in Mice Deficient for miR-34b/c and miR-449 Loci

Comazzetto, S., Di Giacomo, M., Rasmussen, K. D., Much, C., Azzi, C., Perlas, E., Morgan, M. & O'Carroll, D., 16 Oct 2014, In : PLoS Genetics. 10, 10

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60 Citations (Scopus)
90 Downloads (Pure)

Phosphorylated DegU Manipulates Cell Fate Differentiation in the Bacillus subtilis Biofilm

Marlow, V. L., Porter, M., Hobley, L., Kiley, T. B., Swedlow, J. R., Davidson, F. A. & Stanley-Wall, N. R., Jan 2014, In : Journal of Bacteriology. 196, 1, p. 16-27 10 p.

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22 Citations (Scopus)
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Phosphorylation of Sli15 by Ipl1 is important for proper CPC localization and chromosome stability in Saccharomyces cerevisiae

Makrantoni, V., Corbishley, S., Rachidi, N., Morrice, N. A., Robinson, D. A. & Stark, M. J. R., 18 Feb 2014, In : PLoS ONE. 9, 2, 15 p., e89399.

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9 Citations (Scopus)
119 Downloads (Pure)

PITX1, a specificity determinant in the HIF-1α-mediated transcriptional response to hypoxia

Mudie, S., Bandarra, D., Batie, M., Biddlestone, J., Moniz, S., Ortmann, B., Shmakova, A. & Rocha, S., 15 Dec 2014, In : Cell Cycle. 13, 24, p. 3878-3891 14 p.

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10 Citations (Scopus)
163 Downloads (Pure)

PML isoforms in response to arsenic: high-resolution analysis of PML body structure and degradation

Hands, K. J., Cuchet-Lourenco, D., Everett, R. D. & Hay, R. T., 15 Jan 2014, In : Journal of Cell Science. 127, 2, p. 365-375 11 p.

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24 Citations (Scopus)
220 Downloads (Pure)

Prohibitin is required for transcriptional repression by the WT1-BASP1 complex

Toska, E., Shandilya, J., Goodfellow, S. J., Medler, K. F. & Roberts, S. G. E., 23 Oct 2014, In : Oncogene. 33, 43, p. 5100-5108 9 p.

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18 Citations (Scopus)

Proteome-wide identification of SUMO2 modification sites

Tammsalu, T., Matic, I., Jaffray, E. G., Ibrahim, A. F. M., Tatham, M. H. & Hay, R. T., 29 Apr 2014, In : Science Signaling. 7, 323, 10 p., rs2.

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115 Citations (Scopus)

Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control

Bizarro, J., Charron, C., Boulon, S., Westman, B., Pradet-Balade, B., Vandermoere, F., Chagot, M-E., Hallais, M., Ahmad, Y., Leonhardt, H., Lamond, A., Manival, X., Branlant, C., Charpentier, B., Verheggen, C. & Bertrand, E., 24 Nov 2014, In : Journal of Cell Biology. 207, 4, p. 463-480 18 p.

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31 Citations (Scopus)
233 Downloads (Pure)

Proteomic Selection of Immunodiagnostic Antigens for Trypanosoma congolense

Fleming, J. R., Sastry, L., Crozier, T. W. M., Napier, G. B., Sullivan, L. & Ferguson, M. A. J., 2014, In : PLoS Neglected Tropical Diseases. 8, 6, e2936.

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6 Citations (Scopus)
336 Downloads (Pure)